# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:07:05 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: 2-{3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(N)=NCCC[C@@H]1NC(=O)[C@@H]2CCCN2C1=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 ALJ  ALJ  2-{3-[(3S,8aS)-1,4-dioxooctahydropyrrolo[1,2-a]pyrazin-3-yl]propyl}guanidine  ligand  37  18  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ALJ
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 ALJ  O     O  O     0  -0.494  -2.4873  -0.1312   1.7149
 ALJ  C     C  C     0   0.592  -1.2817   0.0653   1.7548
 ALJ  NP    N  NR5   0  -0.496  -0.5746   0.0464   2.8861
 ALJ  CDP   C  CH2   0  -0.255  -1.1519  -0.2594   4.1902
 ALJ  CGP   C  CH2   0  -0.499   0.0174  -0.0468   5.1498
 ALJ  CBP   C  CH2   0  -0.455   1.2522  -0.3088   4.2919
 ALJ  CAP   C  CR15  0  -0.194   0.8573   0.3053   2.9553
 ALJ  CP    C  C     0   0.555   1.5848  -0.2526   1.7533
 ALJ  OP    O  O     0  -0.483   2.7318  -0.6634   1.8217
 ALJ  N     N  NH1   0  -0.644   0.8581  -0.2355   0.6276
 ALJ  CA    C  CH1   0  -0.199  -0.4534   0.3834   0.5119
 ALJ  CB    C  CH2   0  -0.451  -1.1420  -0.0690  -0.7670
 ALJ  CG    C  CH2   0  -0.445  -0.4792   0.4572  -2.0347
 ALJ  CD    C  CH2   0  -0.327  -1.2677   0.0693  -3.2865
 ALJ  NE    N  N     0  -0.484  -0.7159   0.6291  -4.4944
 ALJ  CZ    C  C     0   0.546   0.2205   0.0040  -5.1042
 ALJ  NH1   N  NH2   0  -0.829   0.8225   0.5899  -6.1984
 ALJ  NH2   N  NH2   0  -0.836   0.7206  -1.2391  -4.8027
 ALJ  HDP1  H  HCH2  0   0.247  -1.5099  -1.2915   4.2077
 ALJ  HDP2  H  HCH2  0   0.254  -1.9980   0.3927   4.4082
 ALJ  HGP1  H  HCH2  0   0.261  -0.0418  -0.7051   6.0150
 ALJ  HGP2  H  HCH2  0   0.246   0.0236   0.9822   5.5142
 ALJ  HBP1  H  HCH2  0   0.248   1.4202  -1.3817   4.1784
 ALJ  HBP2  H  HCH2  0   0.262   2.1591   0.1353   4.6965
 ALJ  HAP   H  HCR5  0   0.298   1.0448   1.3891   2.9758
 ALJ  H     H  HNH1  0   0.405   1.3153  -0.5364  -0.2213
 ALJ  HA    H  HCH1  0   0.287  -0.3468   1.4781   0.4759
 ALJ  HBC1  H  HCH2  0   0.251  -2.1722   0.2880  -0.7366
 ALJ  HBC2  H  HCH2  0   0.241  -1.1911  -1.1617  -0.7843
 ALJ  HGC1  H  HCH2  0   0.214   0.5474   0.0890  -2.1340
 ALJ  HGC2  H  HCH2  0   0.229  -0.4077   1.5476  -1.9857
 ALJ  HDC1  H  HCH2  0   0.223  -2.2873   0.4502  -3.1716
 ALJ  HDC2  H  HCH2  0   0.192  -1.3761  -1.0259  -3.3148
 ALJ  HH11  H  HNH2  0   0.378   1.1407  -0.0437  -6.9160
 ALJ  HH12  H  HNH2  0   0.375   0.2868   1.3524  -6.5817
 ALJ  HH21  H  HNH2  0   0.390   1.6510  -1.4448  -5.1285
 ALJ  HH22  H  HNH2  0   0.396   0.5538  -1.5964  -3.8776

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 ALJ  O    C     double  1.222  0.020  1.222
 ALJ  C    NP    single  1.334  0.020  1.334
 ALJ  C    CA    single  1.527  0.020  1.527
 ALJ  NP   CDP   single  1.459  0.020  1.459
 ALJ  NP   CAP   single  1.457  0.020  1.457
 ALJ  CDP  CGP   single  1.528  0.020  1.528
 ALJ  CDP  HDP1  single  0.970  0.020  1.090
 ALJ  CDP  HDP2  single  0.970  0.020  1.090
 ALJ  CGP  CBP   single  1.526  0.020  1.526
 ALJ  CGP  HGP1  single  0.970  0.020  1.090
 ALJ  CGP  HGP2  single  0.970  0.020  1.090
 ALJ  CBP  CAP   single  1.523  0.020  1.523
 ALJ  CBP  HBP1  single  0.970  0.020  1.090
 ALJ  CBP  HBP2  single  0.970  0.020  1.090
 ALJ  CAP  CP    single  1.512  0.020  1.512
 ALJ  CAP  HAP   single  0.970  0.020  1.090
 ALJ  CP   OP    double  1.220  0.020  1.220
 ALJ  CP   N     single  1.340  0.020  1.340
 ALJ  N    CA    single  1.455  0.020  1.455
 ALJ  N    H     single  0.860  0.020  1.020
 ALJ  CA   CB    single  1.521  0.020  1.521
 ALJ  CA   HA    single  0.970  0.020  1.090
 ALJ  CB   CG    single  1.524  0.020  1.524
 ALJ  CB   HBC1  single  0.970  0.020  1.090
 ALJ  CB   HBC2  single  0.970  0.020  1.090
 ALJ  CG   CD    single  1.529  0.020  1.529
 ALJ  CG   HGC1  single  0.970  0.020  1.090
 ALJ  CG   HGC2  single  0.970  0.020  1.090
 ALJ  CD   NE    single  1.441  0.020  1.441
 ALJ  CD   HDC1  single  0.970  0.020  1.090
 ALJ  CD   HDC2  single  0.970  0.020  1.090
 ALJ  NE   CZ    double  1.280  0.020  1.280
 ALJ  CZ   NH1   single  1.380  0.020  1.380
 ALJ  CZ   NH2   single  1.373  0.020  1.373
 ALJ  NH1  HH11  single  0.890  0.020  1.040
 ALJ  NH1  HH12  single  0.890  0.020  1.040
 ALJ  NH2  HH21  single  0.890  0.020  1.040
 ALJ  NH2  HH22  single  0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 ALJ  CA    C    NP    113.93  3.000
 ALJ  CA    C    O     122.82  3.000
 ALJ  NP    C    O     123.24  3.000
 ALJ  CAP   NP   CDP   112.57  3.000
 ALJ  CAP   NP   C     123.96  3.000
 ALJ  CDP   NP   C     123.46  3.000
 ALJ  HDP2  CDP  HDP1  107.91  3.000
 ALJ  HDP2  CDP  CGP   112.66  3.000
 ALJ  HDP1  CDP  CGP   111.85  3.000
 ALJ  HDP2  CDP  NP    111.13  3.000
 ALJ  HDP1  CDP  NP    110.00  3.000
 ALJ  CGP   CDP  NP    103.27  3.000
 ALJ  HGP2  CGP  HGP1  107.76  3.000
 ALJ  HGP2  CGP  CBP   110.17  3.000
 ALJ  HGP1  CGP  CBP   112.76  3.000
 ALJ  HGP2  CGP  CDP   110.19  3.000
 ALJ  HGP1  CGP  CDP   111.92  3.000
 ALJ  CBP   CGP  CDP   104.02  3.000
 ALJ  HBP2  CBP  HBP1  108.15  3.000
 ALJ  HBP2  CBP  CAP   112.21  3.000
 ALJ  HBP1  CBP  CAP   110.18  3.000
 ALJ  HBP2  CBP  CGP   113.28  3.000
 ALJ  HBP1  CBP  CGP   110.58  3.000
 ALJ  CAP   CBP  CGP   102.38  3.000
 ALJ  HAP   CAP  CP    107.24  3.000
 ALJ  HAP   CAP  CBP   109.67  3.000
 ALJ  CP    CAP  CBP   115.10  3.000
 ALJ  HAP   CAP  NP    110.09  3.000
 ALJ  CP    CAP  NP    111.70  3.000
 ALJ  CBP   CAP  NP    103.00  3.000
 ALJ  N     CP   OP    124.14  3.000
 ALJ  N     CP   CAP   113.72  3.000
 ALJ  OP    CP   CAP   122.14  3.000
 ALJ  H     N    CA    117.90  3.000
 ALJ  H     N    CP    117.17  3.000
 ALJ  CA    N    CP    124.14  3.000
 ALJ  HA    CA   CB    108.19  3.000
 ALJ  HA    CA   N     109.78  3.000
 ALJ  CB    CA   N     110.40  3.000
 ALJ  HA    CA   C     106.64  3.000
 ALJ  CB    CA   C     112.13  3.000
 ALJ  N     CA   C     109.61  3.000
 ALJ  HBC2  CB   HBC1  106.56  3.000
 ALJ  HBC2  CB   CG    110.56  3.000
 ALJ  HBC1  CB   CG    108.72  3.000
 ALJ  HBC2  CB   CA    109.30  3.000
 ALJ  HBC1  CB   CA    107.87  3.000
 ALJ  CG    CB   CA    113.56  3.000
 ALJ  HGC2  CG   HGC1  106.14  3.000
 ALJ  HGC2  CG   CD    108.86  3.000
 ALJ  HGC1  CG   CD    108.89  3.000
 ALJ  HGC2  CG   CB    109.59  3.000
 ALJ  HGC1  CG   CB    111.53  3.000
 ALJ  CD    CG   CB    111.65  3.000
 ALJ  HDC2  CD   HDC1  104.90  3.000
 ALJ  HDC2  CD   NE    113.74  3.000
 ALJ  HDC1  CD   NE    108.03  3.000
 ALJ  HDC2  CD   CG    108.91  3.000
 ALJ  HDC1  CD   CG    107.82  3.000
 ALJ  NE    CD   CG    112.96  3.000
 ALJ  CZ    NE   CD    119.31  3.000
 ALJ  NH2   CZ   NH1   113.55  3.000
 ALJ  NH2   CZ   NE    127.13  3.000
 ALJ  NH1   CZ   NE    119.32  3.000
 ALJ  HH12  NH1  HH11  111.86  3.000
 ALJ  HH12  NH1  CZ    113.02  3.000
 ALJ  HH11  NH1  CZ    115.80  3.000
 ALJ  HH22  NH2  HH21  112.22  3.000
 ALJ  HH22  NH2  CZ    117.59  3.000
 ALJ  HH21  NH2  CZ    116.77  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 ALJ  CONST_01  CA   C    NP   CDP   180.00   0.0  0
 ALJ  CONST_02  CA   C    NP   CAP     0.00   0.0  0
 ALJ  CONST_03  CA   N    CP   CAP     0.00   0.0  0
 ALJ  CONST_04  CDP  NP   C    O       0.00   0.0  0
 ALJ  CONST_05  CAP  NP   C    O     180.00   0.0  0
 ALJ  CONST_06  CA   N    CP   OP    180.00   0.0  0
 ALJ  CONST_07  H    N    CP   CAP   180.00   0.0  0
 ALJ  CONST_08  NH1  CZ   NE   CD    180.00   0.0  0
 ALJ  CONST_09  NH2  CZ   NE   CD      0.00   0.0  0
 ALJ  Var_01    CGP  CDP  NP   C    -175.80  30.0  1
 ALJ  Var_02    CBP  CGP  CDP  NP    -26.86  30.0  1
 ALJ  Var_03    CAP  CBP  CGP  CDP    38.11  30.0  1
 ALJ  Var_04    CD   CG   CB   CA   -175.50  30.0  3
 ALJ  Var_05    NE   CD   CG   CB    176.04  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 ALJ  chir_01  CAP  NP  CBP  CP  negativ
 ALJ  chir_02  CA   N   CB   C   negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 ALJ  plan-1  CD    0.020
 ALJ  plan-1  NE    0.020
 ALJ  plan-1  CZ    0.020
 ALJ  plan-1  NH1   0.020
 ALJ  plan-1  NH2   0.020
 ALJ  plan-1  HH11  0.020
 ALJ  plan-1  HH12  0.020
 ALJ  plan-1  HH21  0.020
 ALJ  plan-1  HH22  0.020
 ALJ  plan-2  O     0.020
 ALJ  plan-2  C     0.020
 ALJ  plan-2  NP    0.020
 ALJ  plan-2  CDP   0.020
 ALJ  plan-2  CAP   0.020
 ALJ  plan-2  CA    0.020
 ALJ  plan-3  CAP   0.020
 ALJ  plan-3  CP    0.020
 ALJ  plan-3  OP    0.020
 ALJ  plan-3  N     0.020
 ALJ  plan-3  CA    0.020
 ALJ  plan-3  H     0.020

